X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fplot.phylo.R;h=da5ebec9d1fb58e74b314da9f24dc6723dd46c28;hb=d1546ec66ff1a8ea123adefebe14f6316c23705f;hp=631fb4dc35029d0b52f94a361cb789cf1a35e0ae;hpb=a03a8c554a6fde0dc4313688e3248bfae2e521e4;p=ape.git diff --git a/R/plot.phylo.R b/R/plot.phylo.R index 631fb4d..da5ebec 100644 --- a/R/plot.phylo.R +++ b/R/plot.phylo.R @@ -1,20 +1,21 @@ -## plot.phylo.R (2010-03-19) +## plot.phylo.R (2011-06-14) ## Plot Phylogenies -## Copyright 2002-2010 Emmanuel Paradis +## Copyright 2002-2011 Emmanuel Paradis ## This file is part of the R-package `ape'. ## See the file ../COPYING for licensing issues. -plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, - node.pos = NULL, show.tip.label = TRUE, - show.node.label = FALSE, edge.color = "black", - edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), - adj = NULL, srt = 0, no.margin = FALSE, - root.edge = FALSE, label.offset = 0, underscore = FALSE, - x.lim = NULL, y.lim = NULL, direction = "rightwards", - lab4ut = "horizontal", tip.color = "black", ...) +plot.phylo <- + function(x, type = "phylogram", use.edge.length = TRUE, + node.pos = NULL, show.tip.label = TRUE, + show.node.label = FALSE, edge.color = "black", + edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), + adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE, + label.offset = 0, underscore = FALSE, x.lim = NULL, + y.lim = NULL, direction = "rightwards", lab4ut = "horizontal", + tip.color = "black", plot = TRUE, ...) { Ntip <- length(x$tip.label) if (Ntip == 1) { @@ -276,8 +277,10 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge } - asp <- if (type %in% c("fan", "radial")) 1 else NA # fix by Klaus Schliep (2008-03-28) + asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12) plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...) + +if (plot) { if (is.null(adj)) adj <- if (phyloORclado && direction == "leftwards") 1 else 0 if (phyloORclado && show.tip.label) { @@ -288,7 +291,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, } if (direction == "leftwards") { lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj) - #xx <- xx + MAXSTRING + ##xx <- xx + MAXSTRING } if (!horizontal) { psr <- par("usr") @@ -351,36 +354,59 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, y.adj[sel] <- strheight(x$tip.label)[sel] / 2 sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75 - text(xx[1:Ntip] + x.adj*cex, yy[1:Ntip] + y.adj*cex, + text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex, x$tip.label, adj = c(adj, 0), font = font, srt = srt, cex = cex, col = tip.color) } else { # if lab4ut == "axial" - adj <- as.numeric(abs(XY$axe) > pi/2) - srt <- 180*XY$axe/pi - srt[as.logical(adj)] <- srt[as.logical(adj)] - 180 + adj <- abs(XY$axe) > pi/2 + srt <- 180 * XY$axe / pi + srt[adj] <- srt[adj] - 180 + adj <- as.numeric(adj) + xx.tips <- xx[1:Ntip] + yy.tips <- yy[1:Ntip] + if (label.offset) { + xx.tips <- xx.tips + label.offset * cos(XY$axe) + yy.tips <- yy.tips + label.offset * sin(XY$axe) + } ## `srt' takes only a single value, so can't vectorize this: + ## (and need to 'elongate' these vectors:) + font <- rep(font, length.out = Ntip) + tip.color <- rep(tip.color, length.out = Ntip) + cex <- rep(cex, length.out = Ntip) for (i in 1:Ntip) - text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i], - font = font, srt = srt[i], col = tip.color[i]) + text(xx.tips[i], yy.tips[i], cex = cex[i], + x$tip.label[i], adj = adj[i], font = font[i], + srt = srt[i], col = tip.color[i]) } } if (type %in% c("fan", "radial")) { xx.tips <- xx[1:Ntip] + yy.tips <- yy[1:Ntip] ## using atan2 considerably facilitates things compared to acos... - angle <- atan2(yy[1:Ntip], xx.tips)*180/pi + angle <- atan2(yy.tips, xx.tips) # in radians + if (label.offset) { + xx.tips <- xx.tips + label.offset * cos(angle) + yy.tips <- yy.tips + label.offset * sin(angle) + } s <- xx.tips < 0 + angle <- angle * 180/pi # switch to degrees angle[s] <- angle[s] + 180 - adj <- numeric(Ntip) - adj[xx.tips < 0] <- 1 + adj <- as.numeric(s) ## `srt' takes only a single value, so can't vectorize this: + ## (and need to 'elongate' these vectors:) + font <- rep(font, length.out = Ntip) + tip.color <- rep(tip.color, length.out = Ntip) + cex <- rep(cex, length.out = Ntip) for (i in 1:Ntip) - text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex, - srt = angle[i], adj = adj[i], col = tip.color[i]) + text(xx.tips[i], yy.tips[i], x$tip.label[i], font = font[i], + cex = cex[i], srt = angle[i], adj = adj[i], + col = tip.color[i]) } } if (show.node.label) - text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)], - x$node.label, adj = adj, font = font, srt = srt, cex = cex) + text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)], + x$node.label, adj = adj, font = font, srt = srt, cex = cex) +} L <- list(type = type, use.edge.length = use.edge.length, node.pos = node.pos, show.tip.label = show.tip.label, show.node.label = show.node.label, font = font, @@ -587,3 +613,78 @@ plot.multiPhylo <- function(x, layout = 1, ...) } for (i in 1:length(x)) plot(x[[i]], ...) } + +trex <- function(phy, title = TRUE, subbg = "lightyellow3", + return.tree = FALSE, ...) +{ + lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv) + devmain <- dev.cur() # where the main tree is plotted + + restore <- function() { + dev.set(devmain) + assign("last_plot.phylo", lastPP, envir = .PlotPhyloEnv) + } + + on.exit(restore()) + NEW <- TRUE + cat("Click close to a node. Right-click to exit.\n") + repeat { + x <- identify.phylo(phy, quiet = TRUE) + if (is.null(x)) return(invisible(NULL)) else { + x <- x$nodes + if (is.null(x)) cat("Try again!\n") else { + if (NEW) { + dev.new() + par(bg = subbg) + devsub <- dev.cur() + NEW <- FALSE + } else dev.set(devsub) + + tr <- extract.clade(phy, x) + plot(tr, ...) + if (is.character(title)) title(title) + else if (title) { + tl <- + if (is.null(phy$node.label)) + paste("From node #", x, sep = "") + else paste("From", phy$node.label[x - Ntip(phy)]) + title(tl) + } + if (return.tree) return(tr) + restore() + } + } + } +} + +kronoviz <- function(x, layout = length(x), horiz = TRUE, ...) +{ + par(mar = rep(0.5, 4), oma = rep(2, 4)) + rts <- sapply(x, function(x) branching.times(x)[1]) + maxrts <- max(rts) + lim <- cbind(rts - maxrts, rts) + Ntree <- length(x) + Ntips <- sapply(x, Ntip) + if (horiz) { + nrow <- layout + w <- 1 + h <- Ntips + } else { + nrow <- 1 + w <- Ntips + h <- 1 + } + layout(matrix(1:layout, nrow), widths = w, heights = h) + if (layout > Ntree && !par("ask")) { + par(ask = TRUE) + on.exit(par(ask = FALSE)) + } + if (horiz) { + for (i in 1:Ntree) + plot(x[[i]], x.lim = lim[i, ], ...) + } else { + for (i in 1:Ntree) + plot(x[[i]], y.lim = lim[i, ], direction = "u", ...) + } + axisPhylo(if (horiz) 1 else 4) # better if the deepest tree is last ;) +}